Running nphase partial with a .bam file or a .sam file that isn't sorted or has a header

[OmarOakheart]

Currently nphase partial fails if you don't provide the perfect formal for mapped longReads. I'll close this issue when I've updated it to automatically detect if the user submits a .bam or .sam file and to process it accordingly.

If you run into any issue and you use nphase partial with a mapped long read file, follow these steps:

samtools view -h -t reference.fa -@ threadNumber -F 260 longReads.bam -o longReads.sam samtools sort longReads.sam -@ threadNumber -o longReads.sorted.sam samtools view longReads.sorted.sam -@ threadNumber -o longReads.sorted.noHeader.sam

Then re-run your command and replace longReads.bam with longReads.sorted.noHeader.sam